Single-case designs are a class of research designs for evaluating intervention effects on individual cases. The designs are widely applied in certain fields, including special education, school psychology, clinical psychology, social work, and applied behavior analysis. The multiple baseline design (MBD) is the most frequently used single-case design, and is often described as having desirable internal validity characteristics. This paper examines how the use of certain hierarchical linear models that have been proposed for the MBD affect internal validity, focusing specifically on the two key features described above. First, the author considers a deliberate but non-random method of treatment assignment. I demonstrate that the treatment effect estimate from a conventional multi-level model can be biased under this mechanism, then provide an expression for the magnitude of the bias. Second, he argues that the main analytic models proposed for the MBD fail to capture the benefits of staggered treatment introduction. The author proposes an alternative model that does account for this key feature and, based on the model, he defines an index measuring the strength of control offered by the MBD. A table and figure are appended.